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comparison tools/maf/interval_maf_to_merged_fasta.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 #!/usr/bin/env python
2
3 """
4 Reads an interval or gene BED and a MAF Source.
5 Produces a FASTA file containing the aligned intervals/gene sequences, based upon the provided coordinates
6
7 Alignment blocks are layered ontop of each other based upon score.
8
9 usage: %prog maf_file [options]
10 -d, --dbkey=d: Database key, ie hg17
11 -c, --chromCol=c: Column of Chr
12 -s, --startCol=s: Column of Start
13 -e, --endCol=e: Column of End
14 -S, --strandCol=S: Column of Strand
15 -G, --geneBED: Input is a Gene BED file, process and join exons as one region
16 -t, --mafSourceType=t: Type of MAF source to use
17 -m, --mafSource=m: Path of source MAF file, if not using cached version
18 -I, --mafIndex=I: Path of precomputed source MAF file index, if not using cached version
19 -i, --interval_file=i: Input interval file
20 -o, --output_file=o: Output MAF file
21 -p, --species=p: Species to include in output
22 -O, --overwrite_with_gaps=O: Overwrite bases found in a lower-scoring block with gaps interior to the sequence for a species.
23 -z, --mafIndexFileDir=z: Directory of local maf_index.loc file
24
25 usage: %prog dbkey_of_BED comma_separated_list_of_additional_dbkeys_to_extract comma_separated_list_of_indexed_maf_files input_gene_bed_file output_fasta_file cached|user GALAXY_DATA_INDEX_DIR
26 """
27
28 #Dan Blankenberg
29 from galaxy import eggs
30 from galaxy.tools.util import maf_utilities
31 import pkg_resources; pkg_resources.require( "bx-python" )
32 from bx.cookbook import doc_optparse
33 import bx.intervals.io
34 import sys
35
36 assert sys.version_info[:2] >= ( 2, 4 )
37
38 def stop_err( msg ):
39 sys.stderr.write( msg )
40 sys.exit()
41
42 def __main__():
43
44 #Parse Command Line
45 options, args = doc_optparse.parse( __doc__ )
46 mincols = 0
47 strand_col = -1
48
49 if options.dbkey:
50 primary_species = options.dbkey
51 else:
52 primary_species = None
53 if primary_species in [None, "?", "None"]:
54 stop_err( "You must specify a proper build in order to extract alignments. You can specify your genome build by clicking on the pencil icon associated with your interval file." )
55
56 include_primary = True
57 secondary_species = maf_utilities.parse_species_option( options.species )
58 if secondary_species:
59 species = list( secondary_species ) # make copy of species list
60 if primary_species in secondary_species:
61 secondary_species.remove( primary_species )
62 else:
63 include_primary = False
64 else:
65 species = None
66
67 if options.interval_file:
68 interval_file = options.interval_file
69 else:
70 stop_err( "Input interval file has not been specified." )
71
72 if options.output_file:
73 output_file = options.output_file
74 else:
75 stop_err( "Output file has not been specified." )
76
77 if not options.geneBED:
78 if options.chromCol:
79 chr_col = int( options.chromCol ) - 1
80 else:
81 stop_err( "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes." )
82
83 if options.startCol:
84 start_col = int( options.startCol ) - 1
85 else:
86 stop_err( "Start column not set, click the pencil icon in the history item to set the metadata attributes." )
87
88 if options.endCol:
89 end_col = int( options.endCol ) - 1
90 else:
91 stop_err( "End column not set, click the pencil icon in the history item to set the metadata attributes." )
92
93 if options.strandCol:
94 strand_col = int( options.strandCol ) - 1
95
96 mafIndexFile = "%s/maf_index.loc" % options.mafIndexFileDir
97
98 overwrite_with_gaps = True
99 if options.overwrite_with_gaps and options.overwrite_with_gaps.lower() == 'false':
100 overwrite_with_gaps = False
101
102 #Finish parsing command line
103
104 #get index for mafs based on type
105 index = index_filename = None
106 #using specified uid for locally cached
107 if options.mafSourceType.lower() in ["cached"]:
108 index = maf_utilities.maf_index_by_uid( options.mafSource, mafIndexFile )
109 if index is None:
110 stop_err( "The MAF source specified (%s) appears to be invalid." % ( options.mafSource ) )
111 elif options.mafSourceType.lower() in ["user"]:
112 #index maf for use here, need to remove index_file when finished
113 index, index_filename = maf_utilities.open_or_build_maf_index( options.mafSource, options.mafIndex, species = [primary_species] )
114 if index is None:
115 stop_err( "Your MAF file appears to be malformed." )
116 else:
117 stop_err( "Invalid MAF source type specified." )
118
119 #open output file
120 output = open( output_file, "w" )
121
122 if options.geneBED:
123 region_enumerator = maf_utilities.line_enumerator( open( interval_file, "r" ).readlines() )
124 else:
125 region_enumerator = enumerate( bx.intervals.io.NiceReaderWrapper( open( interval_file, 'r' ), chrom_col = chr_col, start_col = start_col, end_col = end_col, strand_col = strand_col, fix_strand = True, return_header = False, return_comments = False ) )
126
127 #Step through intervals
128 regions_extracted = 0
129 line_count = 0
130 for line_count, line in region_enumerator:
131 try:
132 if options.geneBED: #Process as Gene BED
133 try:
134 starts, ends, fields = maf_utilities.get_starts_ends_fields_from_gene_bed( line )
135 #create spliced alignment object
136 alignment = maf_utilities.get_spliced_region_alignment( index, primary_species, fields[0], starts, ends, strand = '+', species = species, mincols = mincols, overwrite_with_gaps = overwrite_with_gaps )
137 primary_name = secondary_name = fields[3]
138 alignment_strand = fields[5]
139 except Exception, e:
140 print "Error loading exon positions from input line %i: %s" % ( line_count, e )
141 continue
142 else: #Process as standard intervals
143 try:
144 #create spliced alignment object
145 alignment = maf_utilities.get_region_alignment( index, primary_species, line.chrom, line.start, line.end, strand = '+', species = species, mincols = mincols, overwrite_with_gaps = overwrite_with_gaps )
146 primary_name = "%s(%s):%s-%s" % ( line.chrom, line.strand, line.start, line.end )
147 secondary_name = ""
148 alignment_strand = line.strand
149 except Exception, e:
150 print "Error loading region positions from input line %i: %s" % ( line_count, e )
151 continue
152
153 #Write alignment to output file
154 #Output primary species first, if requested
155 if include_primary:
156 output.write( ">%s.%s\n" %( primary_species, primary_name ) )
157 if alignment_strand == "-":
158 output.write( alignment.get_sequence_reverse_complement( primary_species ) )
159 else:
160 output.write( alignment.get_sequence( primary_species ) )
161 output.write( "\n" )
162 #Output all remainging species
163 for spec in secondary_species or alignment.get_species_names( skip = primary_species ):
164 if secondary_name:
165 output.write( ">%s.%s\n" % ( spec, secondary_name ) )
166 else:
167 output.write( ">%s\n" % ( spec ) )
168 if alignment_strand == "-":
169 output.write( alignment.get_sequence_reverse_complement( spec ) )
170 else:
171 output.write( alignment.get_sequence( spec ) )
172 output.write( "\n" )
173
174 output.write( "\n" )
175
176 regions_extracted += 1
177
178 except Exception, e:
179 print "Unexpected error from input line %i: %s" % ( line_count, e )
180 continue
181
182 #close output file
183 output.close()
184
185 #remove index file if created during run
186 maf_utilities.remove_temp_index_file( index_filename )
187
188 #Print message about success for user
189 if regions_extracted > 0:
190 print "%i regions were processed successfully." % ( regions_extracted )
191 else:
192 print "No regions were processed successfully."
193 if line_count > 0 and options.geneBED:
194 print "This tool requires your input file to conform to the 12 column BED standard."
195
196 if __name__ == "__main__": __main__()